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I have seen similar many years ago, its a total PITA to troubleshoot. It may be worth tying to Append the file into a new project?PDFs are built a bit like a filing cabinet, maybe some of the group is being put into the wrong compartment?Another thing to look at is that your Blacks and Whites are not mixed RGB and CMYK, if something is incorrectly converted it could switch Black to White or opposite.